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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgagtaaaccacaaagcatctttggaacacaaatcattttcccttttttacttcgtcttttcttgggaaactggagttaaaagtaggatgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGGCTCATGTCTATCCCAGATGATGGGACCACTGCTAG

Basic information

species Vitis vinifera
transcript Vv01s0127g00720.t01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0127g00720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G03720.6 (Glycine max), 3'ss of exon 6
---------gatgagtaaaccacaaagcatctttggaacacaaatcattttcccttttttacttcgtcttttcttgggaaactggagttaaaagtaggatgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGGCTCATGTCTATCCCAGATGATGGGACCACTGCTAG-------------
          ||   | |||   || |  | |||  ||    | ||    |  |||||||  |  | | ||| ||  ||  ||   |      |||  ||    | |||||||||||||||||||| ||||||||||| || |||||||| ||||||||||||||||||||||||||||| ||||||||||| ||             
tgtagcaaatatagatgaacggaaacgtctttttctaa----attcgaaatagctttttttttgtgccatttttttagattctaatg-----ggtattataacttgcagGTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGGCTCATGTCTATCCCAGATGACGGGACCACTGCAAGGCAAGTCTTATAC

upper sequence: Vv01s0127g00720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA01G03720.2 (Glycine max), 3'ss of exon 8
---------gatgagtaaaccacaaagcatctttggaacacaaatcattttcccttttttacttcgtcttttcttgggaaactggagttaaaagtaggatgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGGCTCATGTCTATCCCAGATGATGGGACCACTGCTAG
          ||   | |||   || |  | |||  ||    | ||    |  |||||||  |  | | ||| ||  ||  ||   |      |||  ||    | |||||||||||||||||||| ||||||||||| || |||||||| ||||||||||||||||||||||||||||| ||||||||||| ||
tgtagcaaatatagatgaacggaaacgtctttttctaa----attcgaaatagctttttttttgtgccatttttttagattctaatg-----ggtattataacttgcagGTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGGCTCATGTCTATCCCAGATGACGGGACCACTGCAAG

upper sequence: Vv01s0127g00720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA02G03990.1 (Glycine max), 3'ss of exon 7
----------gatgagtaaaccacaaagcatctttggaacacaaatcattttcccttttttacttcgtcttttcttgggaaactggagttaaaagtaggatgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGGCTCATGTCTATCCCAGATGATGGGACCACTGCTAG
          | |   | ||    | | | |||||    |  ||| |    |  | |||||  |  | ||||| ||  ||  ||   |      |||  ||    |  ||||||||||||||||||| ||||||||||| || |||||||| ||||||||||||||||||||||||||||| ||||||||||| ||
tatttttatagtttgatgaaa-gtagaacgtcttttt--ctaaaaacggaatagcatttttggt--gccttttttttagattctaatg-----ggtattataacttgaagGTGGAGAATATTGTAGTTATTGGACACAGTTGCTGTGGAGGTATAAAGGGGCTCATGTCTATCCCAGATGACGGGACCACTGCAAG

upper sequence: Vv01s0127g00720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA08G39510.1 (Glycine max), 3'ss of exon 6
--gatgagtaaaccacaaagcatctttggaacacaaatcattttccct--tttttacttcgtcttttcttgggaaactggagttaaaagtaggatgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGGCTCATGTCTATCCCAGATGATGGGACCACTGCTAG
     ||   |  |||| |    ||||       ||| |   |    |    |||  || || | || || |     ||  |||  ||   | ||||  |  |||||||||||||||| |||||||| |||||||| |||||||| |||||||| || ||||||||||||||||||||||||||||| ||
gcacagaaggatgcacagaatggctttcttttttaaaactactagaatagccttttatttgtttcttttttg----ttgtggttctaaagggaatgtcttatagGTGGAGAATATTGTGGTCATTGGGCACAGCTGCTGTGGAGGTATAAAGGGCCTAATGTCTATCCCAGATGATGGGACCACTGCAAG

upper sequence: Vv01s0127g00720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: GLYMA18G19080.1 (Glycine max), 3'ss of exon 5
gatgagtaaaccacaaagcatctttggaacacaaatcattttcccttttttactt-cgtcttttcttgggaaactggagttaaaagtaggatgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGGCTCATGTCTATCCCAGATGATGGGACCACTGCTAG
  | |||     |  ||| ||     |||  |   || ||||      |  | |  | | |||| ||       ||  |||  ||   | ||||  |  |||||||||||||||| ||||||||||||||||| |||||||| |||||||| |||||                              
-gttagtggtgtaagaaggatgaacagaatgcctttcttttttaaaactagaatagcctttttttttttttttttgtggttctaaagtgaatgttttatagGTGGAGAATATTGTGGTCATTGGACACAGCTGCTGTGGAGGTATAAAGGGCCTCAT------------------------------

upper sequence: Vv01s0127g00720.t01 (Vitis vinifera), 3'ss of exon 6
lower sequence: AT1G23730.1 (Arabidopsis thaliana), 3'ss of exon 6
gatgagtaaaccacaaagcatctttggaacacaaatcattttcccttttttacttcgtcttttcttgggaaactggagttaaaagtaggatgtgct--tcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGGCTCATGTCTATCCCAGATGATGGGACCACTGCTAG---
| |||    |||       | |  |  ||   |  ||   |     | || ||        |  ||| |    || || |||    | | |||  |  |||||||||||| ||| | || |||||||||||||||||||| || |||||||| |||||| | ||   |||| ||    |  |  |||    
gttgatgtgacctagttctaaccctaaaaaggaggtc-cctaaaagtgttcaccaaaaaaataattgagcc-ttgtagataatgtaatgctgtcattatcagGTGGAGAACATTCTTGTTATTGGACACAGCTGTTGTGGTGGAATAAAGGGACTCATGGCCATTGAAGATAATACAGCTCCCACTAAGAC

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|30322888|gb|CD006150.1|CD006150
EST:     AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAG                         GTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
genomic: AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAGgtgaatatta ... tgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
EST: gi|34547687|gb|CF515919.1|CF515919
EST:     AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAG                         GTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
genomic: AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAGgtgaatatta ... tgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
EST: gi|110378531|gb|EC943668.1|EC943668
EST:     AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAG                         GTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
genomic: AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAGgtgaatatta ... tgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
EST: gi|110410367|gb|EC976048.1|EC976048
EST:     AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAG                         GTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
genomic: AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAGgtgaatatta ... tgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
EST: gi|110367537|gb|EC931474.1|EC931474
EST:     AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAG                         GTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
genomic: AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAGgtgaatatta ... tgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
EST: gi|32271842|gb|CD721001.1|CD721001
EST:     AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAG                         GTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
genomic: AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAGgtgaatatta ... tgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
EST: gi|34548812|gb|CF517044.1|CF517044
EST:     AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAG                         GTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
genomic: AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAGgtgaatatta ... tgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
EST: gi|225387936|gb|GO307567.1|GO307567
EST:     AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGGAG                         GTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
genomic: AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAGgtgaatatta ... tgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
EST: gi|71859278|gb|DT008333.1|DT008333
EST:     AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAG                         GTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
genomic: AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAGgtgaatatta ... tgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
EST: gi|161715637|gb|FC066795.1|FC066795
EST:     AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAG                         GTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
genomic: AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAGgtgaatatta ... tgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
EST: gi|32248004|gb|CD713823.1|CD713823
EST:     AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAG                         GTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
genomic: AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAGgtgaatatta ... tgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
EST: gi|30328347|gb|CD011609.1|CD011609
EST:     AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAG                         GTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
genomic: AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAGgtgaatatta ... tgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
EST: gi|34548905|gb|CF517137.1|CF517137
EST:     AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAG                         GTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
genomic: AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAGgtgaatatta ... tgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
EST: gi|30128124|gb|CB913463.1|CB913463
EST:     AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAG                         GTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
genomic: AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAGgtgaatatta ... tgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
EST: gi|110387082|gb|EC951724.1|EC951724
EST:     AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAG                         GTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG
genomic: AATACTCTGGAGTTGGGGCGGCCATTGAATATGCAGTATTGCATCTGAAGgtgaatatta ... tgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttacttcgtcttttcttgggaaactggagttaaaagtaggatgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGGCTCATGTCTATCCCAGATGATGGGACCACTGCTAG
                                 ttaaaagta  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgagtaaaccacaaagcatctttggaacacaaatcattttcccttttttacttcgtcttttcttgggaaactggagttaaaagtaggatgtgcttcagGTGGAGAATATTGTAGTCATTGGACACAGCTGTTGTGGAGGGATAAAGGGGCTCATGTCTATCCCAGATGATGGGACCACTGCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - ccacaaa
- - - - - - - - - - - - - - -cacaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggaaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagta